3VFL

Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb3VFL/pdb
• Entry: 3VFL supersedes: 3H5D

• Classification: LYASE
• Organism(s): Streptococcus pneumoniae SP3-BS71
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-10 Released: 2013-06-12 
• Deposition Author(s): Gorman, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.212 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Literature

Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae

Dogovski, C., Gorman, M.A., Ketaren, N.E., Praszkier, J., Bryant, G., Yang, J., Griffin, M.D.W., Pearce, F.G., Bhargava, S.K., Dobson, R.C.J., Hutton, C.A., Gerrard, J.A., Robins-Browne, R.M., Jameson, G.B., Parker, M.W., Perugini, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.81 kDa 
• Atom Count: 5,014 
• Modelled Residue Count: 614 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	311	Streptococcus pneumoniae SP3-BS71	Mutation(s): 0  Gene Names: CGSSp3BS71_00085, dapA EC: 4.2.1.52

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	H [auth A], L [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], G [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	C [auth A], D [auth A], I [auth B], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.212 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.357	α = 90
b = 105.332	β = 90
c = 105.51	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-12 
Deposition Author(s): Gorman, M.A.
• This entry supersedes: 3H5D

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description